# The FixedDegree String kernel takes as input two strings of same size and counts the number of matches of length d.

library("sg")

size_cache <- 10

fm_train_dna <- as.matrix(read.table('../data/fm_train_dna.dat'))
fm_test_dna <- as.matrix(read.table('../data/fm_test_dna.dat'))

# Fixed Degree String
print('FixedDegreeString')

degree <- 3

dump <- sg('set_kernel', 'FIXEDDEGREE', 'CHAR', size_cache, degree)

dump <- sg('set_features', 'TRAIN', fm_train_dna, 'DNA')
km <- sg('get_kernel_matrix', 'TRAIN')

dump <- sg('set_features', 'TEST', fm_test_dna, 'DNA')
km <- sg('get_kernel_matrix', 'TEST')
